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| # Copyright (C) 2002, Thomas Hamelryck ([email protected]) | |
| # | |
| # This file is part of the Biopython distribution and governed by your | |
| # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". | |
| # Please see the LICENSE file that should have been included as part of this | |
| # package. | |
| """Class that maps (chain_id, residue_id) to a residue property.""" | |
| class AbstractPropertyMap: | |
| """Define base class, map holder of residue properties.""" | |
| def __init__(self, property_dict, property_keys, property_list): | |
| """Initialize the class.""" | |
| self.property_dict = property_dict | |
| self.property_keys = property_keys | |
| self.property_list = property_list | |
| def _translate_id(self, entity_id): | |
| """Return entity identifier (PRIVATE).""" | |
| return entity_id | |
| def __contains__(self, id): | |
| """Check if the mapping has a property for this residue. | |
| :param chain_id: chain id | |
| :type chain_id: char | |
| :param res_id: residue id | |
| :type res_id: char | |
| Examples | |
| -------- | |
| This is an incomplete but illustrative example:: | |
| if (chain_id, res_id) in apmap: | |
| res, prop = apmap[(chain_id, res_id)] | |
| """ | |
| translated_id = self._translate_id(id) | |
| return translated_id in self.property_dict | |
| def __getitem__(self, key): | |
| """Return property for a residue. | |
| :param chain_id: chain id | |
| :type chain_id: char | |
| :param res_id: residue id | |
| :type res_id: int or (char, int, char) | |
| :return: some residue property | |
| :rtype: anything (can be a tuple) | |
| """ | |
| translated_id = self._translate_id(key) | |
| return self.property_dict[translated_id] | |
| def __len__(self): | |
| """Return number of residues for which the property is available. | |
| :return: number of residues | |
| :rtype: int | |
| """ | |
| return len(self.property_dict) | |
| def keys(self): | |
| """Return the list of residues. | |
| :return: list of residues for which the property was calculated | |
| :rtype: [(chain_id, res_id), (chain_id, res_id),...] | |
| """ | |
| return self.property_keys | |
| def __iter__(self): | |
| """Iterate over the (entity, property) list. | |
| Handy alternative to the dictionary-like access. | |
| :return: iterator | |
| Examples | |
| -------- | |
| >>> entity_property_list = [ | |
| ... ('entity_1', 'property_1'), | |
| ... ('entity_2', 'property_2') | |
| ... ] | |
| >>> map = AbstractPropertyMap({}, [], entity_property_list) | |
| >>> for (res, property) in iter(map): | |
| ... print(res, property) | |
| entity_1 property_1 | |
| entity_2 property_2 | |
| """ | |
| for i in range(0, len(self.property_list)): | |
| yield self.property_list[i] | |
| class AbstractResiduePropertyMap(AbstractPropertyMap): | |
| """Define class for residue properties map.""" | |
| def __init__(self, property_dict, property_keys, property_list): | |
| """Initialize the class.""" | |
| AbstractPropertyMap.__init__(self, property_dict, property_keys, property_list) | |
| def _translate_id(self, ent_id): | |
| """Return entity identifier on residue (PRIVATE).""" | |
| chain_id, res_id = ent_id | |
| if isinstance(res_id, int): | |
| ent_id = (chain_id, (" ", res_id, " ")) | |
| return ent_id | |
| class AbstractAtomPropertyMap(AbstractPropertyMap): | |
| """Define class for atom properties map.""" | |
| def __init__(self, property_dict, property_keys, property_list): | |
| """Initialize the class.""" | |
| AbstractPropertyMap.__init__(self, property_dict, property_keys, property_list) | |
| def _translate_id(self, ent_id): | |
| """Return entity identifier on atoms (PRIVATE).""" | |
| if len(ent_id) == 4: | |
| chain_id, res_id, atom_name, icode = ent_id | |
| else: | |
| chain_id, res_id, atom_name = ent_id | |
| icode = None | |
| if isinstance(res_id, int): | |
| ent_id = (chain_id, (" ", res_id, " "), atom_name, icode) | |
| return ent_id | |